LAMMPS (1 Feb 2014)
# Rhodopsin model

newton off
package 	gpu force/neigh 0 1 1

variable	x index 2
variable	y index 2
variable	z index 2

units           real
neigh_modify    delay 5 every 1

atom_style      full
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
pair_style      lj/charmm/coul/long/gpu 8.0 10.0
pair_modify     mix arithmetic
kspace_style    pppm/gpu 1e-4

read_data       data.rhodo
  orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  32000 atoms
  reading velocities ...
  32000 velocities
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  18 = max angles/atom
  scanning dihedrals ...
  40 = max dihedrals/atom
  scanning impropers ...
  4 = max impropers/atom
  reading bonds ...
  27723 bonds
  reading angles ...
  40467 angles
  reading dihedrals ...
  56829 dihedrals
  reading impropers ...
  1034 impropers
  4 = max # of 1-2 neighbors
  12 = max # of 1-3 neighbors
  24 = max # of 1-4 neighbors
  26 = max # of special neighbors

replicate	$x $y $z
replicate	2 $y $z
replicate	2 2 $z
replicate	2 2 2
  orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
  1 by 2 by 2 MPI processor grid
  256000 atoms
  221784 bonds
  323736 angles
  454632 dihedrals
  8272 impropers
  4 = max # of 1-2 neighbors
  12 = max # of 1-3 neighbors
  24 = max # of 1-4 neighbors
  26 = max # of special neighbors

fix             1 all shake 0.0001 5 0 m 1.0 a 232
  12936 = # of size 2 clusters
  29064 = # of size 3 clusters
  5976 = # of size 4 clusters
  33864 = # of frozen angles
fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1

special_bonds   charmm

thermo          100
thermo_style    multi
timestep        2.0

run		200
PPPM initialization ...
  G vector (1/distance) = 0.245959
  grid = 48 64 60
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0410392
  estimated relative force accuracy = 0.000123588
  using double precision FFTs
  3d grid and FFT values/proc = 68635 46080
Memory usage per processor = 250.358 Mbytes
---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
TotEng   =    157024.0504 KinEng   =    172792.6155 Temp     =       301.1796 
PotEng   =    -15768.5651 E_bond   =     28164.9917 E_angle  =    117224.0742 
E_dihed  =     61174.8491 E_impro  =      3752.0273 E_vdwl   =     10108.6323 
E_coul   =   1894295.6635 E_long   =  -2130488.8032 Press    =      9562.1557 
Volume   =   2457390.7959 
---------------- Step      100 ----- CPU =     12.3409 (sec) ----------------
TotEng   =   -233301.6797 KinEng   =    123222.9259 Temp     =       214.7790 
PotEng   =   -356524.6057 E_bond   =     13098.4672 E_angle  =     56766.9111 
E_dihed  =     45556.8240 E_impro  =      1313.9378 E_vdwl   =    -40863.9278 
E_coul   =   1705084.7688 E_long   =  -2137481.5867 Press    =     -1634.3910 
Volume   =   2522232.6302 
---------------- Step      200 ----- CPU =     23.6590 (sec) ----------------
TotEng   =   -308341.9699 KinEng   =    108937.4196 Temp     =       189.8792 
PotEng   =   -417279.3895 E_bond   =      9579.0134 E_angle  =     47373.6274 
E_dihed  =     39847.4807 E_impro  =       967.6755 E_vdwl   =    -23635.2996 
E_coul   =   1646633.5046 E_long   =  -2138045.3916 Press    =     -1185.9299 
Volume   =   2554683.1519 
Loop time of 23.6591 on 4 procs for 200 steps with 256000 atoms

Pair  time (%) = 4.81669 (20.3587)
Bond  time (%) = 6.52579 (27.5826)
Kspce time (%) = 4.48765 (18.968)
Neigh time (%) = 1.3238 (5.5953)
Comm  time (%) = 0.490551 (2.07342)
Outpt time (%) = 0.000454485 (0.00192098)
Other time (%) = 6.01414 (25.42)

FFT time (% of Kspce) = 1.77734 (39.6051)
FFT Gflps 3d (1d only) = 5.02949 11.6654

Nlocal:    64000 ave 64001 max 63999 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost:    70656.5 ave 70660 max 70654 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 7.43187
Neighbor list builds = 31
Dangerous builds = 12

Please see the log.cite file for references relevant to this simulation

